Issues

• Vectorize _overlayPoints with NumPy

  Task

  openmm/pdbfixer#358 · Filter by author awjdean opened on Oct 23, 2026

• Added side chains can face the wrong way because the template fit includes the backbone O

  openmm/pdbfixer#356 · Filter by author awjdean opened on Oct 23, 2026

• Update Manual & README with applyMutations feature

  openmm/pdbfixer#353 · Filter by author sbpatel2009 opened on Aug 16, 2026

• Mixed chirality residues produced when loop building

  openmm/pdbfixer#352 · Filter by author Sahil-Athalye opened on Aug 5, 2026
  1

• Gaps are not filled after a residue is mutated

  openmm/pdbfixer#350 · Filter by author dww100 opened on Jul 29, 2026
  1

• ValueError: No template found for N-terminal residue in large multi-chain system (150 chains)

  openmm/pdbfixer#345 · Filter by author Parwez4436 opened on Jan 22, 2026
  4

• Impossible to add missing atoms

  openmm/pdbfixer#341 · Filter by author Mohamed-dev0 opened on Nov 8, 2025
  3

• pdb file

  openmm/pdbfixer#337 · Filter by author Tha57 opened on Aug 24, 2025
  1

• Adding new modified aminoacids

  enhancement
  openmm/pdbfixer#335 · Filter by author andressanchezr4 opened on Jun 25, 2025
  3

• Fixing statistics

  openmm/pdbfixer#334 · Filter by author wangjiawen2013 opened on May 26, 2025
  1

• Application scenario of pdbfixer

  openmm/pdbfixer#333 · Filter by author wangjiawen2013 opened on May 26, 2025
  1

• Residues with various alternative locations remain in the structure

  openmm/pdbfixer#332 · Filter by author dargen3 opened on Apr 30, 2025
  1

• addMissingAtoms additional params

  openmm/pdbfixer#331 · Filter by author scschneider44 opened on Mar 25, 2025
  8

• PDBFixer problems with prepare_receptor4 from ADT

  openmm/pdbfixer#330 · Filter by author groponp opened on Mar 15, 2025
  1

• Non-unified processing of cysteine residues

  openmm/pdbfixer#326 · Filter by author beautifulpie opened on Mar 7, 2025
  1

• PDBFixer - in some cases added residues have amides with non-trans OCNH stereochemistry

  bug
  openmm/pdbfixer#307 · Filter by author ivanicj opened on Sep 30, 2024
  14

• Weird coordinates and unable to add Hydrogens upon adding tyrosines

  openmm/pdbfixer#304 · Filter by author sukritsingh opened on Aug 20, 2024
  5

• Should PDBFixer write out SEQRES entries if provided in the input?

  openmm/pdbfixer#293 · Filter by author sukritsingh opened on Jun 6, 2024
  9

• The repair of two ends of peptide didn't return the desired result

  openmm/pdbfixer#283 · Filter by author bdx114514 opened on Dec 6, 2023

• PDBFixer cannot handle nucleic acids with residue name N

  openmm/pdbfixer#281 · Filter by author jamesmkrieger opened on Nov 14, 2023
  5

• Do we have method to mutate the iCode-containing residue?

  enhancement
  openmm/pdbfixer#280 · Filter by author locitran opened on Oct 11, 2023
  2

• PDBs from RCSB failed to reconstruct

  openmm/pdbfixer#219 · Filter by author slawek111 opened on Mar 30, 2021
  7

• Charges lost on ASP and GLU residues

  openmm/pdbfixer#210 · Filter by author tdudgeon opened on Oct 12, 2020
  1

• How to select a single position for atoms with multiple alternate positions listed

  enhancement
  openmm/pdbfixer#205 · Filter by author ghost opened on Aug 13, 2020
  3

• Residue number strange behavior

  openmm/pdbfixer#201 · Filter by author MauriceKarrenbrock opened on Apr 16, 2020
  2